org.broadinstitute.hellbender.utils.codecs

Class ProgressReportingDelegatingCodec<A extends htsjdk.tribble.Feature,B>

java.lang.Object

org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec<A,B>

All Implemented Interfaces:

htsjdk.tribble.FeatureCodec<A,B>

public final class ProgressReportingDelegatingCodec<A extends htsjdk.tribble.Feature,B>
extends java.lang.Object
implements htsjdk.tribble.FeatureCodec<A,B>

This class is useful when we want to report progress when indexing. The indexing code is in htsjdk and not available to us directly. The workaround is to make a special decorator 'codec' that gets called on every decoded Feature and this can use used to track progress. The codec delegates all calls and reports progress as it goes.

Constructor Summary

Constructors

Constructor and Description
ProgressReportingDelegatingCodec()
ProgressReportingDelegatingCodec(htsjdk.tribble.FeatureCodec<A,B> delegatee, double secondsBetweenUpdates)

Method Summary

Modifier and Type	Method and Description
boolean	canDecode(java.lang.String path)
void	close(B b)
A	decode(B b)
htsjdk.tribble.Feature	decodeLoc(B b)
htsjdk.tribble.FeatureCodec<A,B>	getDelegatee()
java.lang.Class<A>	getFeatureType()
htsjdk.tribble.index.tabix.TabixFormat	getTabixFormat()
boolean	isDone(B b)
htsjdk.samtools.util.LocationAware	makeIndexableSourceFromStream(java.io.InputStream bufferedInputStream)
B	makeSourceFromStream(java.io.InputStream bufferedInputStream)
htsjdk.tribble.FeatureCodecHeader	readHeader(B b)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ProgressReportingDelegatingCodec

public ProgressReportingDelegatingCodec()

ProgressReportingDelegatingCodec

public ProgressReportingDelegatingCodec(htsjdk.tribble.FeatureCodec<A,B> delegatee,
                                        double secondsBetweenUpdates)

Method Detail

decodeLoc

public htsjdk.tribble.Feature decodeLoc(B b)
                                 throws java.io.IOException

Specified by:

decodeLoc in interface htsjdk.tribble.FeatureCodec<A extends htsjdk.tribble.Feature,B>

Throws:

java.io.IOException

decode

public A decode(B b)
         throws java.io.IOException

Specified by:

decode in interface htsjdk.tribble.FeatureCodec<A extends htsjdk.tribble.Feature,B>

Throws:

java.io.IOException

readHeader

public htsjdk.tribble.FeatureCodecHeader readHeader(B b)
                                             throws java.io.IOException

Specified by:

readHeader in interface htsjdk.tribble.FeatureCodec<A extends htsjdk.tribble.Feature,B>

Throws:

java.io.IOException

getFeatureType

public java.lang.Class<A> getFeatureType()

Specified by:

getFeatureType in interface htsjdk.tribble.FeatureCodec<A extends htsjdk.tribble.Feature,B>

makeSourceFromStream

public B makeSourceFromStream(java.io.InputStream bufferedInputStream)

Specified by:

makeSourceFromStream in interface htsjdk.tribble.FeatureCodec<A extends htsjdk.tribble.Feature,B>

makeIndexableSourceFromStream

public htsjdk.samtools.util.LocationAware makeIndexableSourceFromStream(java.io.InputStream bufferedInputStream)

Specified by:

makeIndexableSourceFromStream in interface htsjdk.tribble.FeatureCodec<A extends htsjdk.tribble.Feature,B>

isDone

public boolean isDone(B b)

Specified by:

isDone in interface htsjdk.tribble.FeatureCodec<A extends htsjdk.tribble.Feature,B>

close

public void close(B b)

Specified by:

close in interface htsjdk.tribble.FeatureCodec<A extends htsjdk.tribble.Feature,B>

canDecode

public boolean canDecode(java.lang.String path)

Specified by:

canDecode in interface htsjdk.tribble.FeatureCodec<A extends htsjdk.tribble.Feature,B>

getDelegatee

public htsjdk.tribble.FeatureCodec<A,B> getDelegatee()

getTabixFormat

public htsjdk.tribble.index.tabix.TabixFormat getTabixFormat()

Specified by:

getTabixFormat in interface htsjdk.tribble.FeatureCodec<A extends htsjdk.tribble.Feature,B>